The potential of antimicrobial peptides as Covid-۱۹ therapeutics using computational methods

Background: A new type of coronavirus was first detected in December ۲۰۱۹ at Wuhan city, China. Thepneumonia-like disease caused by the virus is globally known as COVID-۱۹. Apart from China, COVID-۱۹has spread to ۲۱۳ countries and killed over ۵,۷۳۵,۱۷۹ people in total as of today (۷ February ۲۰۲۲). With thecase count and death toll rising each day, there is an urgent need for antiviral drugs against SARS-CoV-۲.Antimicrobial peptides (AMPs) have been widely regarded as a promising solution to combat harmfulmicroorganisms. They are biologically active molecules produced by different organisms as an essentialcomponent of their innate immune response against invading pathogens.Materials and Methods: ۱۱۰ antimicrobial peptides with a length of ۵ to ۵۰ amino acids have been chosenfrom DBAASP and the third structure of proteins have modeled by pepfold۳ server. Then peptides have beenrefined by MODELLER. The structure of SARS_CoV_۲ spike protein has been obtained from protein databank (PDBID:۶lzg). Spike’s ligand has been deleted by Chimera and non-polar hydrogens have been mergedby autodock tools.Finally, peptide files and receptor files have been loaded on pyrx, and docking was carried out for the spikeprotein with the grid box set to center x-, y-, z-axis values of −۴۰.۳۴, ۳۰.۸۵, ۶.۶۱ with a dimension of ۳۵ Åx ۵۰ Å x ۳۰ Å.Result: For binding affinity, the best result was the ۱۵۲۸۸-spike complex with -۱۱.۵ Kj/mol. Then thiscomplex was subsequently analyzed by MD simulation. RMSD, RMSF, and potential energy analysis wereperformed by gromacs.Conclusion: Our results and studies show that a number of peptides in this library have the ability to bind tothe spike protein. This interaction has the potential to disturb the function of the virus and these peptides canbe used as a therapeutic agent.

Keywords:

Molecular Dynamic , Docking , Antimicrobial peptide , Coronavirus , Spike protein